Contacts of the helix formed by residues 224 - 233 (chain A) in PDB entry 1T8U
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 224 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A THR* 3.2 9.0 - - + +
223A ARG* 1.3 91.4 + - + +
225A ALA* 1.3 64.7 + - - +
226A PRO* 3.5 0.9 - - - -
227A ALA* 3.5 8.6 + - + +
228A ARG* 3.1 61.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A PHE* 4.4 17.0 - - + +
219A TYR* 3.4 25.6 - - + +
222A THR* 2.9 27.7 + - + +
224A GLU* 1.3 77.1 - - - +
226A PRO* 1.3 65.4 - - + +
228A ARG* 3.2 2.8 + - - -
229A ILE* 2.9 29.1 + - + +
298A TRP* 3.8 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A THR 3.3 13.0 - - - +
223A ARG 3.4 13.5 - - - +
224A GLU 3.6 0.9 - - - -
225A ALA* 1.3 91.5 - - + +
227A ALA* 1.3 60.3 + - - +
230A SER* 3.1 25.8 + - - -
297A HIS* 4.6 7.0 - - + +
298A TRP* 3.5 55.6 - - + +
301A HIS* 3.6 27.1 - - + +
302A PHE* 3.4 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ARG 5.7 0.4 - - - +
224A GLU* 3.5 11.1 + - + +
225A ALA 3.3 0.6 - - - -
226A PRO* 1.3 80.0 - - - +
228A ARG* 1.3 64.6 + - + +
230A SER* 3.6 2.5 + - - -
231A ALA* 3.1 23.0 + - - +
301A HIS* 3.8 28.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A PHE* 3.0 48.2 + - + -
189A ASP* 4.2 10.1 + - - +
192A TYR* 3.3 62.9 + - + +
193A ASP* 5.9 1.0 + - - -
222A THR* 5.2 1.0 - - - +
224A GLU* 3.1 48.3 + - + +
225A ALA 3.8 2.2 - - - +
227A ALA* 1.3 74.7 - - + +
229A ILE* 1.3 66.9 + - - +
231A ALA* 3.2 7.0 + - - +
232A MET* 3.2 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ILE* 4.4 8.1 - - + -
158A ILE* 4.3 15.3 - - + -
188A PHE* 3.6 40.2 - - + -
219A TYR* 4.3 7.9 - - + -
225A ALA* 2.9 16.5 + - + +
226A PRO 4.2 0.4 - - - +
228A ARG* 1.3 75.2 - - - +
230A SER* 1.3 64.3 + - - +
232A MET* 3.0 17.4 + - + +
233A SER 3.0 10.7 + - - +
236A THR* 3.9 26.0 + - + +
238A LEU* 4.3 2.5 - - + -
298A TRP* 3.7 28.5 - - + -
302A PHE* 3.8 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A PRO 3.1 18.6 + - - -
227A ALA* 3.8 5.4 - - - -
229A ILE* 1.3 76.5 - - - +
231A ALA* 1.3 63.4 + - - +
233A SER* 3.0 22.8 + - - -
234A LYS* 3.1 32.4 + - - +
301A HIS* 3.7 21.9 + - - +
302A PHE* 3.5 19.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A TYR* 4.8 7.0 - - - +
227A ALA 3.1 14.6 + - - +
228A ARG* 3.4 12.8 - - - +
229A ILE 3.2 0.2 - - - -
230A SER* 1.3 75.4 - - - +
232A MET* 1.3 65.8 + - - +
233A SER* 4.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A LEU* 3.9 30.8 - - + +
153A PRO* 3.5 30.3 - - + +
156A ILE* 4.5 10.5 - - + -
188A PHE* 3.7 26.0 - - + -
196A LEU* 4.0 26.7 - - + +
199A TYR* 3.9 14.8 - - - -
228A ARG 3.2 10.0 + - - +
229A ILE* 3.0 13.3 + - + +
231A ALA* 1.3 79.3 - - - +
233A SER* 1.3 67.0 + - - +
236A THR* 3.8 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ILE 3.0 9.4 + - - +
230A SER* 3.0 8.9 + - - +
231A ALA 4.4 0.4 - - - -
232A MET* 1.3 88.5 - - - +
234A LYS* 1.3 59.8 + - - +
235A ASP* 3.1 24.9 + - - +
236A THR* 2.8 34.3 + - - -
302A PHE* 4.2 0.5 - - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il